Jiggy-Ninja:
What happened to the green power LED during this incident? If that also went out, you were probably shorting 5V to GND somehow when you turned the power bar on or accidentally applying the 12V to a place where it shouldn't be. If some of the experimentation in #6 involved rewiring some things in the project, you might have fixed the problem by accident without knowing. Fixing it by moving from a 2.0 to a 30 USB port certainly doesn't make much sense.
If your 12V supply has only 2 mains pins (no earth pin), it is mains isolated and cannot cause any ground loop issue. It's more likely that you accidentally miswired something.
The green power LED remains on, oddly enough. A possible short was my first thought too, which is why I started disconnecting components until I was left with the circuit in my original post. I'm quite confident that I didn't miswire something, as the only connection was to the ground pin of my Arduino.
To thicken the plot, I've found that if I plug my computer power supply into the same power bar as the Arduino, the Arduino locks up again. If I plug my computer power supply into another outlet, everything is fine. Both power supplies I use for my Arduino are two prong, but my PC power supply is three-pronged (i.e., with a ground pin). Regardless of where the PC power supply is plugged in to, the Arduino always locks up if it's plugged into the USB 3.0 port.
Now, admittedly, my understanding of ground loops isn't particularly strong, but I'm curious about your statement "If your 12V supply has only 2 mains pins (no earth pin), it is mains isolated and cannot cause any ground loop issue". Are you sure that's correct? My understanding is that the negative terminal would be "ground" in this case. Are you certain that the absence of an earth ground negates the possibility of a ground loop? That seems to contradict some of the reading that I've done on the subject.
TomGeorge:
Hi,
Welcome to the forum.
Can you please post a picture of your project?
Can you tell us your electronics, programming, arduino, hardware experience?
Can you please post a copy of your full circuit, in CAD or a picture of a hand drawn circuit in jpg, png?
The diagram you supplied does not even show how or what the Arduino does or is connected to?
What model Arduino do you have?
Thanks.. Tom.. 
Thanks for the welcome! I'm an engineer, although I've been out of school for a while so most of hardware knowledge that I have is a little fuzzy. I write embedded software for aeronautics now, so I would say that my software knowledge is very strong, but my hardware knowledge is pretty poor.
Since you're the second person to ask for more information on my posted circuit, I'm going to clarify this point: the circuit in my original post is all that is connected to the Arduino. Just the negative terminal from the power supply, that's it. There are no other connections or hardware connected to the Arduino, just the single wire into the GND pin. Which is why I came here, as everything I knew about grounding suggested that it should work. As I mentioned in my reply to Grumpy_Mike, I'm happy to provide more information about the circuit if you elaborate on what that might be in this case, because what I posted is all that's connected.
I should have mentioned in my first post that I'm using an Arduino Mega.